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Nucleosomes are the fundamental repeating subunits of all
eukaryote chromatin (except when packaged in sperm). They package
DNA into chromosomes inside the cell nucleus and control gene expression. They are made up of DNA and four pairs of
proteins called histones, and resemble "beads on a string of DNA" when observed with an electron microscope. The nucleosome hypothesis proposed by Don and Ada OlinsOlins AL and Olins DE, "Spheroid Chromatin Units (nu Bodies)", Science (1974); 183: 330 - 332 and
Roger Kornberg McDonald D, "Milestone 9, (1973-1974) The nucleosome hypothesis: An alternative string theory", Nature Milestones: Gene Expression. (2005) Dec 1; http://www.nature.com/milestones/geneexpression/milestones/articles/milegene09.html Kornberg, RD, structure: a repeating unit of histones and DNA", Science. (1974); 184: 868–871 in 1974,was a paradigm shift for understanding eukaryotic gene expression. The proteins that make up the nucleosome are called
histones. Histones H2A, H2B, H3 and H4 are part of the nucleosome while histone H1 is the linker DNA between the two nucleosomes.
Nucleosome role in the nucleus
Nucleosomes appear to serve two major purposes within the cell nucleus. First, they provide the lowest level of compaction which is required to fit dsDNA (double-stranded DNA) into the cell nucleus. Secondly, they are important in the regulation of transcription by preventing RNA polymerase from unnecessarily accessing the
promoter of genes which are not needed by the cell. If the requirements of the cell change,
enzymes known as remodeling factors can remove or change the position of the nucleosome to allow access. Nucleosomes also appear to be major carriers of epigenetically inherited information.
Structure of the core particle
The crystal structure of the nucleosome has currently been determined with a resolution better than 2.0 Å,Davey CA, Sargent DF, Luger K, Maeder AW, Richmond TJ, "Crystal Structure of the Nucleosome Core Particle at 2.8 Å Resolution",
Nature (journal). 1997 Sep 18; 389 (6648): 251-60.
The nucleosome repeats, with some variations and exceptions, roughly every 200
base pairs (bp) throughout eukaryotic chromatin. The nucleosome core particle shown in the figure consists of about 146 bp of dsDNA wrapped in 1.65 left-handed Supercoil around four identical pairs of proteins individually known as
histones and collectively known as the histone octamer. The remaining 50 bp of the repeating unit consists of "linker DNA", dsDNA which separates the core particles.
Each of the four histones (
Histone H2A,
Histone H2B, Histone H3, and Histone H4) share a very similar structural motif consisting of three
alpha helix separated by loops. In solution, histones form pairs with identical copies of themselves and are referred to as dimers or histone-fold pairs. In the case of the H3 and H4 histones, they assemble further into tetramers, an association of two H3-H4 dimers, whereby buried charged groups of the same alpha helix on both of the H3 histones
hydrogen bond to each other. The assembly of a nucleosome core particle occurs first by the attachment of the H3-H4 tetramer onto the dsDNA with the later association of two separate H2A-H2B dimers, a process that is likely to occur in a cooperative manner (i.e. both H2A-H2B dimers assemble onto the tetramer at once).
According to the crystal structure, the histone octamer likely interacts with the dsDNA around it roughly every 10 bp. Each of the four histone dimers contain three regions of interaction with the dsDNA. The central interaction site for each dimer is formed by an alpha helix from each histone in the pair pointing at a single phosphate group on the dsDNA to which they hydrogen bond. At positions 10 bp away on either side, a loop from both histones in the pair converge to hydrogen bond to other single phosphate groups. See the figure on the right for a visual representation. Two other interactions (for a total of 14) occur through the interaction of histone tails from each of the H3 histones. These interactions occur at the entry and exit points of the dsDNA wrapping around the nucleosome and help to clamp these regions onto the core particle.
Analysis of the structure of dsDNA wrapped around the histone octamer suggests that it is predominantly B-form, although more tightly constrained than free DNA due to its interaction with the octamer. Curvature into the superhelix comes primarily when either the minor or the major groove faces the octamer and therefore occurs in spurts of roughly 5 bp. Major groove bending around the octamer occurs smoothly. Minor groove bending is facilitated by arginine side chains inserted into the groove and occurs smoothly around the H3-H4 tetramer, but is kinked around the H2A/H2B dimer regions. The DNA is most tightly constrained in regions where it interacts with the double loop structures of the histone dimers mentioned above, which implies that there is more variability in how the DNA interacts with the double alpha helix structures of the histone dimers in order to accommodate the binding of different sequences. Richmond TJ, Davey CA,
Nucleosomes are the fundamental repeating subunits of all
eukaryote chromatin (except when packaged in
sperm). They package
DNA into chromosomes inside the cell nucleus and control gene expression. They are made up of DNA and four pairs of
proteins called
histones, and resemble "beads on a string of DNA" when observed with an
electron microscope. The nucleosome hypothesis proposed by Don and Ada OlinsOlins AL and Olins DE, "Spheroid Chromatin Units (nu Bodies)", Science (1974); 183: 330 - 332 and Roger Kornberg McDonald D, "Milestone 9, (1973-1974) The nucleosome hypothesis: An alternative string theory", Nature Milestones: Gene Expression. (2005) Dec 1; http://www.nature.com/milestones/geneexpression/milestones/articles/milegene09.html Kornberg, RD, structure: a repeating unit of histones and DNA", Science. (1974); 184: 868–871 in 1974,was a paradigm shift for understanding eukaryotic gene expression. The proteins that make up the nucleosome are called histones. Histones H2A, H2B, H3 and H4 are part of the nucleosome while histone H1 is the linker DNA between the two nucleosomes.
Nucleosome role in the nucleus
Nucleosomes appear to serve two major purposes within the cell nucleus. First, they provide the lowest level of compaction which is required to fit dsDNA (double-stranded DNA) into the cell nucleus. Secondly, they are important in the regulation of transcription by preventing RNA polymerase from unnecessarily accessing the promoter of genes which are not needed by the cell. If the requirements of the cell change, enzymes known as remodeling factors can remove or change the position of the nucleosome to allow access. Nucleosomes also appear to be major carriers of epigenetically inherited information.
Structure of the core particle
The crystal structure of the nucleosome has currently been determined with a resolution better than 2.0 Å,Davey CA, Sargent DF, Luger K, Maeder AW, Richmond TJ, "Crystal Structure of the Nucleosome Core Particle at 2.8 Å Resolution",
Nature (journal). 1997 Sep 18; 389 (6648): 251-60.
The nucleosome repeats, with some variations and exceptions, roughly every 200 base pairs (bp) throughout eukaryotic chromatin. The nucleosome core particle shown in the figure consists of about 146 bp of dsDNA wrapped in 1.65 left-handed
Supercoil around four identical pairs of proteins individually known as histones and collectively known as the
histone octamer. The remaining 50 bp of the repeating unit consists of "linker DNA", dsDNA which separates the core particles.
Each of the four histones (
Histone H2A,
Histone H2B,
Histone H3, and
Histone H4) share a very similar structural motif consisting of three alpha helix separated by loops. In solution, histones form pairs with identical copies of themselves and are referred to as dimers or histone-fold pairs. In the case of the H3 and H4 histones, they assemble further into tetramers, an association of two H3-H4 dimers, whereby buried charged groups of the same alpha helix on both of the H3 histones hydrogen bond to each other. The assembly of a nucleosome core particle occurs first by the attachment of the H3-H4 tetramer onto the dsDNA with the later association of two separate H2A-H2B dimers, a process that is likely to occur in a cooperative manner (i.e. both H2A-H2B dimers assemble onto the tetramer at once).
According to the crystal structure, the histone octamer likely interacts with the dsDNA around it roughly every 10 bp. Each of the four histone dimers contain three regions of interaction with the dsDNA. The central interaction site for each dimer is formed by an alpha helix from each histone in the pair pointing at a single phosphate group on the dsDNA to which they hydrogen bond. At positions 10 bp away on either side, a loop from both histones in the pair converge to hydrogen bond to other single phosphate groups. See the figure on the right for a visual representation. Two other interactions (for a total of 14) occur through the interaction of histone tails from each of the H3 histones. These interactions occur at the entry and exit points of the dsDNA wrapping around the nucleosome and help to clamp these regions onto the core particle.
Analysis of the structure of dsDNA wrapped around the histone octamer suggests that it is predominantly B-form, although more tightly constrained than free DNA due to its interaction with the octamer. Curvature into the superhelix comes primarily when either the minor or the major groove faces the octamer and therefore occurs in spurts of roughly 5 bp. Major groove bending around the octamer occurs smoothly. Minor groove bending is facilitated by arginine side chains inserted into the groove and occurs smoothly around the H3-H4 tetramer, but is kinked around the H2A/H2B dimer regions. The DNA is most tightly constrained in regions where it interacts with the double loop structures of the histone dimers mentioned above, which implies that there is more variability in how the DNA interacts with the double alpha helix structures of the histone dimers in order to accommodate the binding of different sequences. Richmond TJ, Davey CA,
Nucleosome - Wikipedia, the free encyclopedia
Nucleosomes are the fundamental repeating units of eukaryotic chromatin, [1] with the exception of mature sperm. [2] They are the smallest structural unit of eukaryotic DNA ...
Edinburgh Nucleosome Positioning Site
Nucleosome Positioning and Computational Biology at Edinburgh University ... Welcome to the Edinburgh Nucleosome Positioning Site (ENPS). The purpose of this repository is to ...
GO:0000786 nucleosome - QuickGO
The European Bioinformatics Institute ... You can reach the search box using alt+9 (Win/IE), alt+shift+9 (Win/Firefox) or ctrl+9 (Mac)
QuickGO: GO Term GO:0006334
Name [?] nucleosome assembly: Last updated [?] 2001-03-30 04:29:44.0: Definition [?] The aggregation, arrangement and bonding together of a nucleosome, the beadlike structural units of ...
Nucleosome
Legend: Nucleosome: Subunit of chromatin composed of a short length of DNA wrapped around a core of histone proteins. The human genome contains about 3 billion nucleotide pairs ...
Nucleosome
Introduction - This script shows the structure nucleosome core particle (Based on 1aoi.pdb, K. Luger et al., Nature 389 251 (1997)).
Nucleosome code
A discussion about the discovery of the nucleosome code. Nucleosome position coded in DNA Sequence Alec MacAndrew. Each of our billions of cells contains about two metres or six ...
Definition: nucleosome from Online Medical Dictionary
The Online Medical Dictionary is a searchable dictionary of definitions from medicine, science and technology.
SCOP: Protein: HAND domain of the nucleosome remodeling ATPase ISWI ...
Protein: HAND domain of the nucleosome remodeling ATPase ISWI from Fruit fly (Drosophila melanogaster) Lineage: Root: scop; Class: All alpha proteins [46456] Fold: HAND domain of ...
AmiGO: nucleosome Details
Term Information Accession GO:0000786 Ontology cellular component Synonyms alt_id: GO:0005718 Definition A complex comprised of DNA wound around a multisubunit core and associated ...
